Solution:
Ok so I figured it out! It appears that woocommerce 2.1 > does not set a cookie at until the cart is used, to help with caching or something. Here is a thread on it : https://github.com/woothemes/woocommerce/issues/4920
Solution for me was to add this to my function :
do_action( 'woocommerce_set_cart_cookies', true );
Hope this helps someone else.